Cells • First law of thermodynamics • Second law of ... · Il ferro è legato, in entrambi i...

Università degli Studi di Verona – Facoltà di Scienze MM. FF. e NN.

Corso di Laurea Triennale in Biotecnologie a.a. 2011-2012 ● Corso di Microbiologia Generale ● Titolare: Prof. Giovanni Vallini

Nutrizione e metabolismo

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• Cells

open, non-equilibrium systems

• First law of thermodynamics

conservation of energy - energy can neither be created nor

destroyed in the universe

• Second law of thermodynamics

energy spontaneously disperses (if it is not hindered

from doing so)

predicts the probability of the dispersal

entropy change measures how much or how widely

energy is spread out in a process

BASIC ENERGY CONCEPTS




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• Greatest good - because of the second law, life is possible

life can take in concentrated energy and use some of that energy to synthesize

"uphill" complex biochemicals and to run highly regulated interdependent processes,

including millions of non-spontaneous reactions

• Biggest bad - because of the second law, life is always threatened

non-spontaneous metabolic reactions are metastable; life cannot function unless a

multitude of "molecular machines” and biochemical cycles operate synchronically in

using energy to oppose second law predictions

SECOND LAW OF THERMODYNAMICS




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• Energy dispersal and diversion of part of the energy flow

Photosynthesizing organisms take certain wavelengths of the sun's

dispersing energy, plus carbon dioxide and water, and make new chemical

compounds that are more complex and more energy-containing

Photosynthesis is in the 30% range; 70% of the sun’s energy is dispersed

to the environment (net entropy increase)

EXAMPLE: PHOTOSYNTHESIS




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• Metabolism

sum total of all reactions that occur in a cell

• Catabolic reactions

break down of complex molecules into smaller, simpler molecules

with the release of energy and reducing power (electrons)

• Anabolic reactions

synthesis of complex molecules from simpler ones

requires energy and reducing power (electrons) to form cell structures

• Catabolic and anabolic reactions

coupled, highly regulated, interdependent, and simultaneous

METABOLISM




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Esempi di agenti chelanti prodotti dai

micoorganismi per il trasporto del

ferro: (a) idrossimato; (b) enterobactina.

Il ferro è legato, in entrambi i casi, come

Fe3+.




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• Activation energy is the innate obstacle to the second law of

thermodynamics in chemical reactions

• Role of biological catalysts

• Metastable patterns among biological structures and processes

are highly regulated by a vast variety of feedback systems

• Example:

storage of energy in ATP is contrary to the predictions of the second law. Energy

within the bonds of the ATP molecule is kept from being dispersed by activation

energy barriers until life needs it for a reaction

HOW CAN LIFE EXIST?




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Progress of a hypothetical reaction: A + B C + D

and the concept of activation energy




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• What is an enzyme?

• Functional enzyme

• Mechanism of enzymatic reaction

“generic” version

one enzyme - many substrates

many enzymes - one substrate

classes of enzymes

• Regulation of enzymes

via synthesis

via activity

ENZYMES




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Ciclo catalitico della fruttosio-difosfato-aldolasi




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ENZYME/CO-ENZYME SYSTEMS




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• Redox reaction

– oxidation: loss of electrons

– reduction: gain of electrons

• Each molecule has the potential to donate

and accept electrons from another molecule

ENERGY PRODUCTION




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Reduction and Oxidation (A)

An atom becomes more reduced when it undergoes a chemical reaction in which it

1) gains electrons

2) by bonding to a less electronegative atom

3) … and often this occurs when the atom becomes bonded to a hydrogen




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Reduction and Oxidation (B)

An atom becomes more oxidized when it undergoes a chemical reaction in which it

1) loses electrons

2) by bonding to a more electronegative atom

3) … and often this occurs when the atom becomes bonded to an oxygen




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Reduction and Oxidation (C)

i) In metabolic pathways, we are often concerned with the oxidation or reduction

of carbon

ii) Reduced forms of carbon (e.g. hydrocarbons, methane, fats, carbohydrates,

alcohols) carry a great deal of potential chemical energy stored in their bonds

iii) Oxidized forms of carbon (e.g. ketones, aldehydes, carboxylic acids, carbon

dioxide) carry very little potential chemical energy in their bonds




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Reduction and Oxidation (D)

Reduction and oxidation always occur together. In a reduction-oxidation reaction

(redox reaction), one substance gets reduced, and another substance gets

oxidized. The thing that gets oxidized is called the electron donor, and the thing

that gets reduced is called the electron acceptor.




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Esempio di reazione di ossido-riduzione




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La torre dei potenziali delle più importanti coppie

redox, ricorrenti in ambito metabolico




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Cofactors for Redox Reactions

(a) Enzymes that catalyze redox reactions typically require a cofactor to

“shuttle” electrons from one part of the metabolic pathway to another

part.

(b) There are two main redox cofactors: NAD and FAD. These are

(relatively) small organic molecules in which part of the structure can

either be reduced (e.g., accept a pair of electrons) or oxidized (e.g.,

donate a pair of electrons).




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Cofactors for Redox Reactions

NAD(oxidized) + H+ + Pair of electrons NADH(reduced)

FAD(oxidized) + H+ + Pair of electrons FADH(reduced)

NAD and FAD are present only in small (catalytic) amounts – they cannot serve

as the final electron acceptor, but must be regenerated (reoxidized) in order for

metabolism to continue




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Struttura delle forme

ossidata e ridotta del

coenzima NAD+/NADP+

Nicotinammide-adenin-dinucleotide




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Rappresentazione schematica di ossido-riduzione mediata da NAD+ e NADH




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ATP

ATP hydrolysis is used as an energy source in many biological reactions that

require energy – for example, active transport in the sodium-potassium pump.

During catabolism, energy released from the oxidation of carbon is captured

and used to synthesize ATP from ADP and phosphate.

C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + Energy

ADP + Phosphate + Energy → ATP + H2O




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ATP: A “currency of energy” for many cellular reactions

ATP stands for adenosine triphosphate. It is a nucleotide with three phosphate

groups linked in a small chain.

The last phosphate in the chain can be removed by hydrolysis (the ATP becomes

ADP, or adenosine diphosphate).

This reaction is energetically favorable: it has a G0' of about – 7.5 kcal/mol

ATP + H2O ADP + Phosphate + Energy (7.5 kcal/mol)

.




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ATP




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Composti importanti nelle reazioni di trasformazione dell’energia

all’interno della cellula microbica




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Conservazione dell’energia nella fermentazione e nella respirazione




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4 major glycolytic pathways found in different bacteria:

1) Embden-Meyerhof-Parnas pathway

“Classic” glycolysis

Found in almost all organisms

2) Hexose monophosphate pathway

Also found in most organisms

Responsible for synthesis of pentose sugars used in nucleotide synthesis

3) Entner-Doudoroff pathway

Found in Pseudomonas and related genera

4) Phosphoketolase pathway

Found in Bifidobacterium and Leuconostoc




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Embden-Meyerhof pathway

(glycolysis)




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Features of glycolytic pathways

a) Partial oxidation of glucose to form pyruvic acid

b) A small amount of ATP is made

c) A small amount of NAD is reduced to NADH

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Hexose Mono-phosphate (HMP)

pathway




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The Entner-Doudoroff pathway

of glucose catabolism in pseudomonads




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The phosphoketolase pathway




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NUCLEOTIDI FLAVINICI




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Il trasportatore di idrogeno flavin-mononucleotide (FMN)




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Struttura dei citocromi




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Ferro-Zolfo proteine non-eme




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Struttura delle forme ossidata e ridotta del coenzima Q




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Catene di trasporto degli elettroni e rispettiva relazione con l’E0’




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Formazione della Proton Motive Force




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Generazione della forza motrice protonica

durante la respirazione aerobica




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Struttura e funzione dell’ATPasi batterica




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L’ATPasi F1F0 in realtà ruota




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La sintesi di ATP è il frutto di un’attività ATPasica in senso inverso




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Sintesi di ATP via Proton Motive Force




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Movimento dei flagelli spinto dalla Proton Motive Force




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Trasporto transmembrana spinto dalla Proton Motive Force




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IL CICLO DEGLI ACIDI TRICARBOSSILICI




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BILANCIO ENERGETICO DELLA RESPIRAZIONE AEROBICA




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Rappresentazione schematica delle reazioni all’interno di una cellula batterica




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Biosintesi degli zuccheri




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Origine biosintetica degli aminoacidi




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GS = glutamine synthase

GOGAT = glutamate synthase

GDH = glutamate deydrogenase

Incorporazione dell’ammonio nei batteri




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Biosintesi delle purine e delle pirimidine




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Biosintesi degli acidi grassi

Cells • First law of thermodynamics • Second law of ... · Il ferro è legato, in entrambi i...

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